[2024-01-24 14:19:15,937] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:15,939] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:15,939] [INFO] DQC Reference Directory: /var/lib/cwl/stg27f3e042-0fa7-4dc5-a10c-c92d33228177/dqc_reference
[2024-01-24 14:19:17,203] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:17,204] [INFO] Task started: Prodigal
[2024-01-24 14:19:17,204] [INFO] Running command: gunzip -c /var/lib/cwl/stg9653a05f-0ae5-4495-bf00-28fe1e3fb0a1/GCF_005144715.1_ASM514471v1_genomic.fna.gz | prodigal -d GCF_005144715.1_ASM514471v1_genomic.fna/cds.fna -a GCF_005144715.1_ASM514471v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:27,138] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:27,139] [INFO] Task started: HMMsearch
[2024-01-24 14:19:27,139] [INFO] Running command: hmmsearch --tblout GCF_005144715.1_ASM514471v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27f3e042-0fa7-4dc5-a10c-c92d33228177/dqc_reference/reference_markers.hmm GCF_005144715.1_ASM514471v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:27,415] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:27,417] [INFO] Found 6/6 markers.
[2024-01-24 14:19:27,463] [INFO] Query marker FASTA was written to GCF_005144715.1_ASM514471v1_genomic.fna/markers.fasta
[2024-01-24 14:19:27,464] [INFO] Task started: Blastn
[2024-01-24 14:19:27,464] [INFO] Running command: blastn -query GCF_005144715.1_ASM514471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27f3e042-0fa7-4dc5-a10c-c92d33228177/dqc_reference/reference_markers.fasta -out GCF_005144715.1_ASM514471v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:28,533] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:28,537] [INFO] Selected 20 target genomes.
[2024-01-24 14:19:28,538] [INFO] Target genome list was writen to GCF_005144715.1_ASM514471v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:28,549] [INFO] Task started: fastANI
[2024-01-24 14:19:28,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg9653a05f-0ae5-4495-bf00-28fe1e3fb0a1/GCF_005144715.1_ASM514471v1_genomic.fna.gz --refList GCF_005144715.1_ASM514471v1_genomic.fna/target_genomes.txt --output GCF_005144715.1_ASM514471v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:45,211] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:45,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27f3e042-0fa7-4dc5-a10c-c92d33228177/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:45,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27f3e042-0fa7-4dc5-a10c-c92d33228177/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:45,236] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:45,236] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:45,237] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	100.0	1089	1089	95	conclusive
Sphingomonas yantingensis	strain=DSM 27244	GCA_014199325.1	1241761	1241761	type	True	81.2092	629	1089	95	below_threshold
Sphingomonas spermidinifaciens	strain=9NM-10	GCA_002351485.1	1141889	1141889	type	True	81.094	635	1089	95	below_threshold
Sphingomonas japonica	strain=DSM 22753	GCA_011762085.1	511662	511662	type	True	80.6189	565	1089	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	80.3238	557	1089	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	80.2578	570	1089	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	79.7536	538	1089	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.5616	504	1089	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	79.5348	546	1089	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.5164	537	1089	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	79.4923	480	1089	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	79.4679	528	1089	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	79.4363	458	1089	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.3474	538	1089	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	79.2128	459	1089	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	79.2073	480	1089	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.2035	516	1089	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	79.153	504	1089	95	below_threshold
Sphingomonas palmae	strain=JS21-1	GCA_900109565.1	1855283	1855283	type	True	79.0148	443	1089	95	below_threshold
Sphingomonas radiodurans	strain=S9-5	GCA_020866845.1	2890321	2890321	type	True	78.6979	461	1089	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:45,239] [INFO] DFAST Taxonomy check result was written to GCF_005144715.1_ASM514471v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:45,240] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:45,240] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:45,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27f3e042-0fa7-4dc5-a10c-c92d33228177/dqc_reference/checkm_data
[2024-01-24 14:19:45,241] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:45,276] [INFO] Task started: CheckM
[2024-01-24 14:19:45,277] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005144715.1_ASM514471v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005144715.1_ASM514471v1_genomic.fna/checkm_input GCF_005144715.1_ASM514471v1_genomic.fna/checkm_result
[2024-01-24 14:20:27,105] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:27,107] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:27,132] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:27,132] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:27,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005144715.1_ASM514471v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:27,133] [INFO] Task started: Blastn
[2024-01-24 14:20:27,134] [INFO] Running command: blastn -query GCF_005144715.1_ASM514471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27f3e042-0fa7-4dc5-a10c-c92d33228177/dqc_reference/reference_markers_gtdb.fasta -out GCF_005144715.1_ASM514471v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:29,141] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:29,146] [INFO] Selected 21 target genomes.
[2024-01-24 14:20:29,146] [INFO] Target genome list was writen to GCF_005144715.1_ASM514471v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:29,163] [INFO] Task started: fastANI
[2024-01-24 14:20:29,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg9653a05f-0ae5-4495-bf00-28fe1e3fb0a1/GCF_005144715.1_ASM514471v1_genomic.fna.gz --refList GCF_005144715.1_ASM514471v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005144715.1_ASM514471v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:46,758] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:46,779] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:46,779] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_005144715.1	s__Sphingomonas sp005144715	100.0	1089	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014199325.1	s__Sphingomonas yantingensis	81.2232	630	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.75	96.75	0.89	0.89	2	-
GCF_002351485.1	s__Sphingomonas spermidinifaciens	81.1084	634	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000786205.1	s__Sphingomonas sp000786205	80.6692	582	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346325.1	s__Sphingomonas japonica	80.5483	575	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001555965.1	s__Sphingomonas sp001555965	80.185	524	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	97.92	0.88	0.78	8	-
GCF_018449795.1	s__Sphingomonas sp018449795	80.0119	542	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744835.1	s__Sphingomonas sp017744835	79.9191	545	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712135.1	s__Sphingomonas sp000712135	79.9082	527	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745215.1	s__Sphingomonas sp017745215	79.8413	540	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428865.1	s__Sphingomonas sp001428865	79.6408	534	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897375.1	s__Sphingomonas sp001897375	79.6049	493	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_004345855.1	s__Sphingomonas sp004345855	79.572	559	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241485.1	s__Sphingomonas sp000241485	79.5493	538	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014194975.1	s__Sphingomonas sp014194975	79.3953	530	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927115.1	s__Sphingomonas sp012927115	79.2839	542	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193845.1	s__Sphingomonas sp014193845	79.2498	539	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
GCF_014197135.1	s__Sphingomonas zeae	79.0092	436	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001598415.1	s__Sphingomonas mali	78.9968	479	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019075875.1	s__Novosphingobium sp019075875	77.8803	347	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232625.1	s__Allosphingosinicella sp019232625	77.7815	357	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	99.90	99.89	0.98	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:46,781] [INFO] GTDB search result was written to GCF_005144715.1_ASM514471v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:46,781] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:46,786] [INFO] DFAST_QC result json was written to GCF_005144715.1_ASM514471v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:46,786] [INFO] DFAST_QC completed!
[2024-01-24 14:20:46,786] [INFO] Total running time: 0h1m31s